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April 21, 2016
Kyoto University

Deep-sea microorganisms preferentially utilize D-amino acids
- Mystery of microorganisms in deep-sea world -


A joint research team by Research and Development Center for Marine Biosciences at the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) and Kyoto University identified microorganisms that preferentially utilize D-amino acids instead of L-amino acids for growth, which were isolated from deep-sea sediments in Sagami Bay by manned submersibles, Shinkai 2000 and Shinkai 6500 and a remotely operated vehicle, ROV Hyper Dolphin during JAMSTEC's expeditions.

Amino acids, which are the structural units that make up proteins, can occur in two isomeric forms; L-amino acids and D-amino acids. They are mirror images of one another with three-dimensional structures (Figure 1). It has been regarded that living organisms preferentially use L-amino acids only. Recent progress of analytical techniques unveiled, however, that D-amino acids are also utilized by all sorts of living creatures from human beings to microorganisms. In particular, since it became clear that D-Serine, one of D-amino acids, regulates higher brain functions in mammals, physiological functions and metabolic pathways of D-amino acids synthesis and degradation are drawing increased attention.

In this study, the research group successfully isolated microorganisms utilizing D-amino acids into 28 strains, which were from deep-sea sediments collected at depth of 800-1,500 m in Sagami Bay between 2001 and 2008. In addition, a deep-sea microorganism that grows D-amino acids most efficiently was compared with closely-related strains isolated from shallow sea (Figure. 2 and 3). The result demonstrated that only the deep-sea isolate have an ability to utilize D-amino acids efficiently, though there are almost no genomic differences between those from deep-sea and shallow sea. It is a remarkable characteristic, suggesting a rapidly acquired strategy of microorganisms to survive in deep-sea as an oligotrophic environment by preferentially utilizing D-amino acids as nutrition, while L-amino-acids are predominant among living creatures in general. Further analysis of deep -sea microorganisms should help clarify D-amino functions still with lots of mysteries, and contribute to development of new medical technology and biotechnology.

The above results were published on Frontiers in Microbiology on April 19, 2016 (JST). The online version is available at:

Enantioselective utilization of D-amino acids by deep-sea microorganisms
Takaaki Kubota1, Tohru Kobayashi1, Takuro Nunoura1, Fumito Maruyama2, Shigeru Deguchi1
1Research and Development Center for Marine Biosciences, JAMSTEC
2Graduate School of Medicine, Kyoto University
Figure 1

Figure 1. L-serine (left) and D-serine (right)

Figure 2

Figure 2. Nautella sp. strain A04V that grows with D-amino acid as a sole major amino acid in the medium.
(The image obtained by Scanning Electron Microscope.)

Figure 3

Figure 3. Growth of Nautella strain A04V with L-valine and D-valine as a sole major amino acid in the growth media.


(For this study)
Takuro Nunoura, Deputy Director-General, Research and Development Center for Marine Biosciences, JAMSTEC
(For press release)
Tsuyoshi Noguchi, Manager, Press Division, Public Relations, JAMSTEC
David Hajime Kornhauser, Director, Global Communications, Kyoto University
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